Thanks. I wonder if this analysis will be reproducible though (they don't mention any parameters...): >"Phylogenetic analysis Phylogenetic relationships were e

Thanks. I wonder if this analysis will be reproducible though (they don't mention any parameters...): >"Phylogenetic analysis Phylogenetic relationships were estimated from comparisons of predicted protein sequences. Sequences were aligned using CLUSTAL (Higgins and Sharp, 1988, 1989). Evolutionary distances between all pairs of sequences were computed using Kimura's empirical method (Kimura, 1983; eqn. 4.8) to estimate the number of superimposed amino acid replacements; sites at which there was a gap in any sequence in the alignment were excluded from all comparisons. Phylogenetic relationships were estimated from these distances by the neighbor-joining method (Saitou and Nei, 1987). The reliability of branching orders was estimated by the bootstrap approach (Felsenstein, 1985). These methods were implemented using CLUSTAL V (Higgins et al., 1992). Nucleotide accession numbers All sequences were submitted to GenBank and are available under accession numbers U03994-U04018." It looks like those sequences are a mixture of the various proteins (env, pol, etc) so it would take some time to figure out which is which. I don't feel it like right now. It seems like getting the sequences from genbank and then aligning using default params with clustalw would be closest to their method. If someone wants to do it: http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/genbank/ http://www.genome.jp/tools/clustalw/ http://www.genome.jp/tools/clustalw/